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The Hocotate Ship first appears in Pikmin 2, replacing the repossessed S.S. Dolphin from the previous game as Olimar's base of operations on the planet of the Pikmin. In addition to providing safety above the planet's surface at night for the explorers, it hosts Purple and White Pikmin, which have no Onions of their own, and dispatches its Research Pod to follow the group underground when necessary. The ship has a haughty personality and often berates Olimar and Louie for their incompetence.

In Super Smash Bros. Brawl, the Hocotate Ship appears as part of Olimar's Final Smash, End of Day. Olimar enters the ship at it launches above the stage as night falls, which causes several Bulborbs to damage the opponents, before falling back down onto the stage and exploding. The Hocotate Ship was also Olimar's means of transportation in the Subspace Emissary, where he is presumed to have piloted it to enter Subspace. The ship can be seen in the background of the Outside the Ancient Ruins level, and the first turquoise cube in that level will always drop the Hocotate Ship trophy.

The Hocotate Bomb, an explosive modeled after the Hocotate Ship, appears as an item in Super Smash Bros. 4. When thrown, it will fly off, and then crash down after a period of time. The Hocotate Ship is also still a part of Olimar's Final Smash.

A battered old spaceship used when Hocotate Freight first opened. Its appraisal gauge analyzed garbage Olimar brought home and found it to be valuable. With his new ship sold off to pay company debts, Louie and Olimar flew this one back to the Pikmin world to find more treasure. The ship's removable research pod accompanied the adventurers when they ventured underground.